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‎src/workflows/annotation/scanvi_scarches/config.vsh.yaml‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,12 @@ authors:
77
- __merge__: /src/authors/weiwei_schultz.yaml
88
roles: [ contributor ]
99

10+
info:
11+
name: "scANVI - scArches workflow"
12+
test_dependencies:
13+
- name: scanvi_scarches_test
14+
namespace: test_workflows/annotation
15+
1016
argument_groups:
1117
- name: Query Input
1218
arguments:

‎target/executable/annotate/celltypist/.config.vsh.yaml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
name: "celltypist"
22
namespace: "annotate"
3-
version: "v2.1.0-rc.1"
3+
version: "2.0.0-rc.1"
44
authors:
55
- name: "Jakub Majercik"
66
roles:
@@ -368,7 +368,7 @@ engines:
368368
- type: "docker"
369369
id: "docker"
370370
image: "python:3.10-slim"
371-
target_tag: "v2.1.0-rc.1"
371+
target_tag: "2.0.0-rc.1"
372372
namespace_separator: "/"
373373
setup:
374374
- type: "apt"
@@ -416,9 +416,9 @@ build_info:
416416
output: "target/executable/annotate/celltypist"
417417
executable: "target/executable/annotate/celltypist/celltypist"
418418
viash_version: "0.9.3"
419-
git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
419+
git_commit: "f7844754a7f22de462f24cc98c2c62967922eeee"
420420
git_remote: "https://github.com/openpipelines-bio/openpipeline"
421-
git_tag: "2.0.0-rc.1-4-g26c00c397a3"
421+
git_tag: "2.0.0-rc.1-5-gf7844754a7f"
422422
package_config:
423423
name: "openpipeline"
424424
info:
@@ -433,8 +433,8 @@ package_config:
433433
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
434434
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
435435
\ := 'includeConfig(\"nextflow_labels.config\")'"
436-
- ".version := \"v2.1.0-rc.1\""
437-
- ".engines[.type == 'docker'].target_tag := 'v2.1.0-rc.1'"
436+
- ".version := \"2.0.0-rc.1\""
437+
- ".engines[.type == 'docker'].target_tag := '2.0.0-rc.1'"
438438
organization: "openpipelines-bio"
439439
links:
440440
repository: "https://github.com/openpipelines-bio/openpipeline"

‎target/executable/annotate/celltypist/celltypist‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# celltypist v2.1.0-rc.1
3+
# celltypist 2.0.0-rc.1
44
#
55
# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -465,10 +465,10 @@ RUN pip install --upgrade pip && \
465465
466466
LABEL org.opencontainers.image.authors="Jakub Majercik, Weiwei Schultz"
467467
LABEL org.opencontainers.image.description="Companion container for running component annotate celltypist"
468-
LABEL org.opencontainers.image.created="2025-04-02T07:57:08Z"
468+
LABEL org.opencontainers.image.created="2025-04-02T11:08:32Z"
469469
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
470-
LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
471-
LABEL org.opencontainers.image.version="v2.1.0-rc.1"
470+
LABEL org.opencontainers.image.revision="f7844754a7f22de462f24cc98c2c62967922eeee"
471+
LABEL org.opencontainers.image.version="2.0.0-rc.1"
472472
473473
VIASHDOCKER
474474
fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
585585

586586
# ViashHelp: Display helpful explanation about this executable
587587
function ViashHelp {
588-
echo "celltypist v2.1.0-rc.1"
588+
echo "celltypist 2.0.0-rc.1"
589589
echo ""
590590
echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of"
591591
echo "logistic regression classifiers optimised by the stochastic gradient descent"
@@ -767,7 +767,7 @@ while [[ $# -gt 0 ]]; do
767767
shift 1
768768
;;
769769
--version)
770-
echo "celltypist v2.1.0-rc.1"
770+
echo "celltypist 2.0.0-rc.1"
771771
exit
772772
;;
773773
--input)
@@ -1087,7 +1087,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
10871087

10881088
# determine docker image id
10891089
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
1090-
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/celltypist:v2.1.0-rc.1'
1090+
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/celltypist:2.0.0-rc.1'
10911091
fi
10921092

10931093
# print dockerfile

‎target/executable/annotate/onclass/.config.vsh.yaml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
name: "onclass"
22
namespace: "annotate"
3-
version: "v2.1.0-rc.1"
3+
version: "2.0.0-rc.1"
44
authors:
55
- name: "Jakub Majercik"
66
roles:
@@ -351,7 +351,7 @@ engines:
351351
- type: "docker"
352352
id: "docker"
353353
image: "python:3.11"
354-
target_tag: "v2.1.0-rc.1"
354+
target_tag: "2.0.0-rc.1"
355355
namespace_separator: "/"
356356
setup:
357357
- type: "python"
@@ -387,9 +387,9 @@ build_info:
387387
output: "target/executable/annotate/onclass"
388388
executable: "target/executable/annotate/onclass/onclass"
389389
viash_version: "0.9.3"
390-
git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
390+
git_commit: "f7844754a7f22de462f24cc98c2c62967922eeee"
391391
git_remote: "https://github.com/openpipelines-bio/openpipeline"
392-
git_tag: "2.0.0-rc.1-4-g26c00c397a3"
392+
git_tag: "2.0.0-rc.1-5-gf7844754a7f"
393393
package_config:
394394
name: "openpipeline"
395395
info:
@@ -404,8 +404,8 @@ package_config:
404404
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
405405
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
406406
\ := 'includeConfig(\"nextflow_labels.config\")'"
407-
- ".version := \"v2.1.0-rc.1\""
408-
- ".engines[.type == 'docker'].target_tag := 'v2.1.0-rc.1'"
407+
- ".version := \"2.0.0-rc.1\""
408+
- ".engines[.type == 'docker'].target_tag := '2.0.0-rc.1'"
409409
organization: "openpipelines-bio"
410410
links:
411411
repository: "https://github.com/openpipelines-bio/openpipeline"

‎target/executable/annotate/onclass/onclass‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# onclass v2.1.0-rc.1
3+
# onclass 2.0.0-rc.1
44
#
55
# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
454454
455455
LABEL org.opencontainers.image.authors="Jakub Majercik"
456456
LABEL org.opencontainers.image.description="Companion container for running component annotate onclass"
457-
LABEL org.opencontainers.image.created="2025-04-02T07:57:08Z"
457+
LABEL org.opencontainers.image.created="2025-04-02T11:08:32Z"
458458
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
459-
LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
460-
LABEL org.opencontainers.image.version="v2.1.0-rc.1"
459+
LABEL org.opencontainers.image.revision="f7844754a7f22de462f24cc98c2c62967922eeee"
460+
LABEL org.opencontainers.image.version="2.0.0-rc.1"
461461
462462
VIASHDOCKER
463463
fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
574574

575575
# ViashHelp: Display helpful explanation about this executable
576576
function ViashHelp {
577-
echo "onclass v2.1.0-rc.1"
577+
echo "onclass 2.0.0-rc.1"
578578
echo ""
579579
echo "OnClass is a python package for single-cell cell type annotation. It uses the"
580580
echo "Cell Ontology to capture the cell type similarity."
@@ -751,7 +751,7 @@ while [[ $# -gt 0 ]]; do
751751
shift 1
752752
;;
753753
--version)
754-
echo "onclass v2.1.0-rc.1"
754+
echo "onclass 2.0.0-rc.1"
755755
exit
756756
;;
757757
--input)
@@ -1066,7 +1066,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
10661066

10671067
# determine docker image id
10681068
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
1069-
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/onclass:v2.1.0-rc.1'
1069+
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/onclass:2.0.0-rc.1'
10701070
fi
10711071

10721072
# print dockerfile

‎target/executable/annotate/popv/.config.vsh.yaml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
name: "popv"
22
namespace: "annotate"
3-
version: "v2.1.0-rc.1"
3+
version: "2.0.0-rc.1"
44
authors:
55
- name: "Matthias Beyens"
66
roles:
@@ -306,7 +306,7 @@ engines:
306306
- type: "docker"
307307
id: "docker"
308308
image: "python:3.11-slim"
309-
target_tag: "v2.1.0-rc.1"
309+
target_tag: "2.0.0-rc.1"
310310
namespace_separator: "/"
311311
setup:
312312
- type: "docker"
@@ -353,9 +353,9 @@ build_info:
353353
output: "target/executable/annotate/popv"
354354
executable: "target/executable/annotate/popv/popv"
355355
viash_version: "0.9.3"
356-
git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
356+
git_commit: "f7844754a7f22de462f24cc98c2c62967922eeee"
357357
git_remote: "https://github.com/openpipelines-bio/openpipeline"
358-
git_tag: "2.0.0-rc.1-4-g26c00c397a3"
358+
git_tag: "2.0.0-rc.1-5-gf7844754a7f"
359359
package_config:
360360
name: "openpipeline"
361361
info:
@@ -370,8 +370,8 @@ package_config:
370370
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
371371
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
372372
\ := 'includeConfig(\"nextflow_labels.config\")'"
373-
- ".version := \"v2.1.0-rc.1\""
374-
- ".engines[.type == 'docker'].target_tag := 'v2.1.0-rc.1'"
373+
- ".version := \"2.0.0-rc.1\""
374+
- ".engines[.type == 'docker'].target_tag := '2.0.0-rc.1'"
375375
organization: "openpipelines-bio"
376376
links:
377377
repository: "https://github.com/openpipelines-bio/openpipeline"

‎target/executable/annotate/popv/popv‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# popv v2.1.0-rc.1
3+
# popv 2.0.0-rc.1
44
#
55
# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -466,10 +466,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git
466466
467467
LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
468468
LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
469-
LABEL org.opencontainers.image.created="2025-04-02T07:57:07Z"
469+
LABEL org.opencontainers.image.created="2025-04-02T11:08:32Z"
470470
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
471-
LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
472-
LABEL org.opencontainers.image.version="v2.1.0-rc.1"
471+
LABEL org.opencontainers.image.revision="f7844754a7f22de462f24cc98c2c62967922eeee"
472+
LABEL org.opencontainers.image.version="2.0.0-rc.1"
473473
474474
VIASHDOCKER
475475
fi
@@ -586,7 +586,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
586586

587587
# ViashHelp: Display helpful explanation about this executable
588588
function ViashHelp {
589-
echo "popv v2.1.0-rc.1"
589+
echo "popv 2.0.0-rc.1"
590590
echo ""
591591
echo "Performs popular major vote cell typing on single cell sequence data using"
592592
echo "multiple algorithms. Note that this is a one-shot version of PopV."
@@ -726,7 +726,7 @@ while [[ $# -gt 0 ]]; do
726726
shift 1
727727
;;
728728
--version)
729-
echo "popv v2.1.0-rc.1"
729+
echo "popv 2.0.0-rc.1"
730730
exit
731731
;;
732732
--input)
@@ -981,7 +981,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
981981

982982
# determine docker image id
983983
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
984-
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/popv:v2.1.0-rc.1'
984+
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/popv:2.0.0-rc.1'
985985
fi
986986

987987
# print dockerfile

‎target/executable/annotate/random_forest_annotation/.config.vsh.yaml‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
name: "random_forest_annotation"
22
namespace: "annotate"
3-
version: "v2.1.0-rc.1"
3+
version: "2.0.0-rc.1"
44
authors:
55
- name: "Jakub Majercik"
66
roles:
@@ -359,7 +359,7 @@ engines:
359359
- type: "docker"
360360
id: "docker"
361361
image: "python:3.12-slim"
362-
target_tag: "v2.1.0-rc.1"
362+
target_tag: "2.0.0-rc.1"
363363
namespace_separator: "/"
364364
setup:
365365
- type: "apt"
@@ -402,9 +402,9 @@ build_info:
402402
output: "target/executable/annotate/random_forest_annotation"
403403
executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation"
404404
viash_version: "0.9.3"
405-
git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
405+
git_commit: "f7844754a7f22de462f24cc98c2c62967922eeee"
406406
git_remote: "https://github.com/openpipelines-bio/openpipeline"
407-
git_tag: "2.0.0-rc.1-4-g26c00c397a3"
407+
git_tag: "2.0.0-rc.1-5-gf7844754a7f"
408408
package_config:
409409
name: "openpipeline"
410410
info:
@@ -419,8 +419,8 @@ package_config:
419419
- ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
420420
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
421421
\ := 'includeConfig(\"nextflow_labels.config\")'"
422-
- ".version := \"v2.1.0-rc.1\""
423-
- ".engines[.type == 'docker'].target_tag := 'v2.1.0-rc.1'"
422+
- ".version := \"2.0.0-rc.1\""
423+
- ".engines[.type == 'docker'].target_tag := '2.0.0-rc.1'"
424424
organization: "openpipelines-bio"
425425
links:
426426
repository: "https://github.com/openpipelines-bio/openpipeline"

‎target/executable/annotate/random_forest_annotation/random_forest_annotation‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env bash
22

3-
# random_forest_annotation v2.1.0-rc.1
3+
# random_forest_annotation 2.0.0-rc.1
44
#
55
# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
66
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
461461
462462
LABEL org.opencontainers.image.authors="Jakub Majercik"
463463
LABEL org.opencontainers.image.description="Companion container for running component annotate random_forest_annotation"
464-
LABEL org.opencontainers.image.created="2025-04-02T07:57:07Z"
464+
LABEL org.opencontainers.image.created="2025-04-02T11:08:32Z"
465465
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
466-
LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
467-
LABEL org.opencontainers.image.version="v2.1.0-rc.1"
466+
LABEL org.opencontainers.image.revision="f7844754a7f22de462f24cc98c2c62967922eeee"
467+
LABEL org.opencontainers.image.version="2.0.0-rc.1"
468468
469469
VIASHDOCKER
470470
fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
581581

582582
# ViashHelp: Display helpful explanation about this executable
583583
function ViashHelp {
584-
echo "random_forest_annotation v2.1.0-rc.1"
584+
echo "random_forest_annotation 2.0.0-rc.1"
585585
echo ""
586586
echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of"
587587
echo "random forest."
@@ -763,7 +763,7 @@ while [[ $# -gt 0 ]]; do
763763
shift 1
764764
;;
765765
--version)
766-
echo "random_forest_annotation v2.1.0-rc.1"
766+
echo "random_forest_annotation 2.0.0-rc.1"
767767
exit
768768
;;
769769
--input)
@@ -1072,7 +1072,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
10721072

10731073
# determine docker image id
10741074
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
1075-
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/random_forest_annotation:v2.1.0-rc.1'
1075+
VIASH_DOCKER_IMAGE_ID='ghcr.io/openpipelines-bio/openpipeline/annotate/random_forest_annotation:2.0.0-rc.1'
10761076
fi
10771077

10781078
# print dockerfile

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